5500XL SOLiD Sequencers
Two massively parallel next-generation sequencing platforms (SOLiD 5500 series) are currently incorporated in users' research for transcriptomics analysis. The platforms can be used for a wide array of applications, such as global gene expression analysis with single base resolution, single-cell or meta-transcriptomic analysis, regulation of gene expression including ChIP-Seq or microRNA analysis, and the identification of novel genes or isoforms. The platforms offer a non-biased, highly quantitative, and accurate method to sequence DNA or RNA from any source and supersede that of previous technologies. Multiple unique samples can be sequenced in parallel in a single run with high coverage using barcoding, saving time and reagents. Because of a novel two-base encoding method that discriminates between actual single nucleotide polymorphisms (SNPs) and sequencing errors, sequencing from normal or mutated cells can identify gene expression or epigenetic (gene methylation analysis) alterations as well as SNPs in a quantitative and accurate manner.
Instrument ID:
34124
Availability: 24 hours a day, 7 days a week
Custodians
| Galya Orr | (509) 371-6127 | Galya.Orr@pnnl.gov |
| Lye Meng Markillie | meng.markillie@pnnl.gov |
Publications
Using high through-put RNA sequencing, we assayed the transcriptomes of three different strains of Toxoplasma gondii representing three common...
Domain Archaea is currently represented by one phylum (Euryarchaeota) and two superphyla (TACK and DPANN). However, gene surveys indicate the...
Diversity begets higher order properties such as functional stability and robustness in microbial communities, but principles that inform conceptual...
We employed deep sequencing technology to identify transcriptional adaptation of the euryhaline unicellular cyanobacterium Synechococcus sp. PCC 7002...
To assess molecular responses to low doses of radiation that may be encountered during medical diagnostic procedures, nuclear accidents, or terrorist...
Geologic carbon dioxide (CO2) sequestration drives physical and geochemical changes in deep subsurface environments that impact indigenous microbial...
Phototrophic microbial mats are compact ecosystems composed of highly interactive organisms in which energy and element cycling take place over...
Lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition....
In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated “Ente-robacter lignolyticus” SCF1 on...
Rapidly fluctuating environmental conditions can significantly stress organisms, particularly when fluctuations cross thresholds of normal...
BD1-5, OP11, and OD1 bacteria have been widely detected in anaerobic environments, but
their metabolisms remain unclear owing to lack of cultivated...
Background: Multiple post-translational modifications (PTMs) on core histones often work synergistically to fine tune chromatin structure and...
The isoprenoid pathway converts pyruvate to isoprene and related isoprenoid compounds in plants and some bacteria. Currently, this pathway is of...
In the G1 phase of the cell division cycle, eukaryotic cells prepare many of the resources necessary for a new round of growth including renewal of...
Removal of selenium from groundwater was documented during injection of acetate into a uraniumcontaminated aquifer near Rifle, Colorado (USA)....
To understand how cell physiological state affects mRNA translation, we used Shewanella oneidensis MR-1 grown under steady state conditions at either...
Toxoplasma gondii infects up to one third of the world’s population. A key to the success of T.gondii is its ability to persist for the...
The anaerobic isolate Enterobacter lignolyticus SCF1 was initially cultivated based on anaerobic growth on lignin as sole carbon source. The source...
Quick Specs
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Science Highlights
Posted: Tuesday, June 14, 2016 - 15:38
The Science
Bacteria have a major impact on natural ecosystems, human health, disease progression and industrial processes using bacterial cultures...
Posted: Friday, April 17, 2015 - 09:16
The Science
Archaea, a domain of single-celled microorganisms, represent a significant fraction of the earth’s biodiversity, yet they remain much...
Projects
Background: In the proposed work we will use a newly developed experimental system comprised of the alga Chrysochromulina tobin (Haptophyceae) and a...
Terrestrial freshwater wetlands are carbon rich environments that play a significant role in the global release of methane to the atmosphere. Our...
The exchange of carbon and other nutrients between microorganisms is a key factor in the establishment of microbial interactions and trophic levels....
Ocean microbes drive the biogeochemistry that fuels the planet, and their viruses impact microbes through mortality, horizontal gene transfer, and...
Dynamic sulfur pools as a control on methane flux in freshwater Prairie Pothole lacustrine sediments
Inland waters (wetlands, lakes) play a poorly constrained role in regional and global carbon cycling, and may account for much of the uncertainty in...